Bioinformatics pertinent to lipid analysis in biological samples

Electrospray ionization mass spectrometry has revolutionized the way lipids are studied. In this work, we present a tutorial for analyzing class-specific lipid spectra obtained from a triple quadrupole mass spectrometer. The open-source software MZmine 2.21 is used, coupled with LIPID MAPS databases. Here, we describe the steps for lipid identification, ratiometric quantification, and briefly address the differences to the analyses when using direct infusion versus tandem liquid chromatography–mass spectrometry (LC–MS). We also provide a tutorial and equations for quantification of lipid amounts using synthetic lipid standards and normalization to a protein amount.